publication
LIB Publications
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Last
updated in July 2012
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2012
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1.
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X Jiao, BT Sherman, R Stephens, MW Baseler, HC Lane, RA Lempicki. DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics (2012) 28 (13): 1805-1806.
doi: 10.1093/bioinformatics/bts251
[PubMed]
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2009
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1.
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Huang DW, Sherman BT, Lempicki
RA. Systematic and integrative analysis of large gene lists using DAVID
Bioinformatics Resources. Nature
Protoc. 2009;4(1):44-57.
[PubMed]
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2.
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Huang DW, Sherman BT, Lempicki
RA. Bioinformatics enrichment tools: paths toward the comprehensive
functional analysis of large gene lists. Nucleic Acids Res. 2009
Jan;37(1):1-13.
[PubMed]
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2008
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1.
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Barton G, Abbott J, Chiba N,
Huang DW, Huang Y, Krznaric M, Mack-Smith J, Saleem A, Sherman BT,
Tiwari B, Tomlinson C, Aitman T, Darlington J, Game L, Sternberg MJ,
Butcher SA. EMAAS: an extensible grid-based rich internet application
for microarray data analysis and management. BMC Bioinformatics. 2008
Nov 25;9:493.
[PubMed]
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2.
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Read SW, Lempicki RA, Di Mascio
M, Srinivasula S, Burke R, Sachau W, Bosche M, Adelsberger JW, Sereti
I, Davey RT Jr, Tavel JA, Huang CY, Issaq HJ, Fox SD, Lane HC, Kovacs
JA. CD4 T cell survival after intermittent interleukin-2 therapy is
predictive of an increase in the CD4 T cell count of HIV-infected
patients. J Infect Dis. 2008 Sep 15;198(6):843-50.
[PubMed]
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3.
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Huang DW, Sherman BT, Lempicki
RA. DAVID gene ID conversion tool. Bioinformation. 2008. July; 2(10):
428-430
[PubMed]
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4.
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Suzman DL, McLaughlin M, Hu Z,
Kleiner DE, Wood B, Lempicki RA, Mican JM, Suffredini A, Masur H, Polis
MA, Kottilil S. Identification of novel markers for liver fibrosis in
HIV/hepatitis C virus coinfected individuals using genomics-based
approach. AIDS. 2008 Jul 31;22(12):1433-9.
[PubMed]
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5.
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Arthos J, Cicala C, Martinelli
E, Macleod K, Van Ryk D, Wei D, Xiao Z, Veenstra TD, Conrad TP,
Lempicki RA, McLaughlin S, Pascuccio M, Gopaul R, McNally J, Cruz CC,
Censoplano N, Chung E, Reitano KN, Kottilil S, Goode DJ, Fauci AS.
HIV-1 envelope protein binds to and signals through integrin
alpha4beta7, the gut mucosal homing receptor for peripheral T cells. Nature Immunol. 2008 Mar;9(3):301-9.
[PubMed]
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6.
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Tilton JC, Manion MM, Luskin MR,
Johnson AJ, Patamawenu AA, Hallahan CW, Cogliano-Shutta NA, Mican JM,
Davey RT Jr, Kottilil S, Lifson JD, Metcalf JA, Lempicki RA, Connors M.
Human immunodeficiency virus viremia induces plasmacytoid dendritic
cell activation in vivo and diminished alpha interferon production in
vitro. J Virol. 2008 Apr;82(8):3997-4006.
[PubMed]
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7.
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Imamichi T, Yang J, Huang DW,
Brann TW, Fullmer BA, Adelsberger JW, Lempicki RA, Baseler MW, Lane HC.
IL-27, a novel anti-HIV cytokine, activates multiple
interferon-inducible genes in macrophages. AIDS. 2008 Jan 2;22(1):39-45.
[PubMed]
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| 2007 |
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1.
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Sherman BT, Huang DW, Tan
Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC,
Lempicki RA. DAVID Knowledgebase: A Gene-centered Database Integrating
Heterogeneous
Gene Annotation Resources to Facilitate High-throughput Gene Functional
Analysis. BMC Bioinformatics. 2007 Nov 2;8(1):426.
[PubMed]
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2.
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Nussenblatt V, McLaughlin M,
Rehm CA, Lempicki RA, Brann T, Yang J,
Proschan M, Highbarger HC, Dewar RL, Imamichi T, Koratich C, Neumann
AU, Masur H, Polis MA, Kottilil S. Immunodeficiency and intrinsic IFN
resistance are associated with viral breakthrough to HCV therapy in
HIV-coinfected patients. AIDS Res Hum Retroviruses. 2007
Nov;23(11):1354-9.
[PubMed]
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3.
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Kottilil S, Jackson JO, Reitano
KN, O'shea MA, Roby G, Lloyd M, Yang J, Hallahan CW, Rehm CA, Arthos J,
Lempicki R, Fauci AS.Innate Immunity in HIV Infection: Enhanced
Susceptibility to CD95-Mediated Natural Killer Cell Death and Turnover
Induced by HIV Viremia. J Acquir Immune Defic Syndr. 2007 Oct
1;46(2):151-9.
[PubMed]
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4.
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Ishaq M, Degray G, Mou K,
Aguilera A, Yang J, Lempicki RA, Hazen A, Natarajan V.
Zap70 signaling pathway mediates glucocorticoid
receptor-dependent transcriptional activation: role in the regulation
of annexin 1 expression in T cells. J Immunol. 2007 Sep
15;179(6):3851-8.
[PubMed]
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5.
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Huang DW, Sherman BT, Tan Q,
Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC,
Lempicki RA. DAVID Gene Functional Classification Tool: A novel
biological
module-centric algorithm to functionally analyze large gene list.
Genome Biol. 2007 Sep 4;8(9):R183.
[PubMed]
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6.
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Huang DW, Sherman BT, Tan Q,
Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC,
Lempicki RA. DAVID Bioinformatics Resources: Expanded annotation
database and
novel algorithms to better extract biology from large gene lists.
Nucleic Acids Res. 2007 Jul 1;35.
[PubMed]
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7.
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Fakruddin JM, Lempicki RA,
Gorelick RJ, Yang J, Adelsberger JW, Garcia-Pineres AJ, Pinto LA, Lane
HC, Imamichi T.
Noninfectious papilloma virus-like particles inhibit HIV-1
replication: implications for immune control of HIV-1 infection by
IL-27. Blood. 2007 Mar 1;109(5):1841-9.
[PubMed]
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| 2006 |
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1.
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Tilton JC, Johnson AJ, Luskin
MR, Manion MM, Yang J, Adelsberger JW, Lempicki RA, Hallahan CW,
McLaughlin M, Mican JM, Metcalf JA, Iyasere C, Connors M. Diminished
production of monocyte proinflammatory cytokines during human
immunodeficiency virus viremia is mediated by type I interferons. J
Virol. 2006 Dec;80(23):11486-97.
[PubMed]
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2.
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Wu L, Kottilil S, Lempicki R,
Yang J, McLaughlin M, Hu Z, Koratich C,
Reitano KN, Rehm CA, Masur H, Wood B, Kleiner DE, Polis MA. Hepatic
histologic response (HR) to combination therapy among
HCV/HIV-coinfected individuals: interferon induces HR independent of
sustained virologic response (SVR). AIDS Res Hum Retroviruses. 2006
Nov;22(11):1091-8.
[PubMed]
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3.
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Bacolla A, Collins JR, Gold B,
Chuzhanova N, Yi M, Stephens RM, Stefanov S, Olsh A, Jakupciak JP, Dean
M, Lempicki RA, Cooper DN, Wells RD. Long homopurine*homopyrimidine
sequences are characteristic of genes expressed in brain and the
pseudoautosomal region. Nucleic Acids Res. 2006 May 19;34(9):2663-75.
[PubMed]
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4.
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Cortez KJ, Lyman CA, Kottilil S,
Kim HS, Roilides E, Yang J, Fullmer B, Lempicki R, Walsh TJ.
Functional genomics of innate host defense molecules in normal human
monocytes in response to Aspergillus fumigatus. Infect Immun. 2006
Apr;74(4):2353-65.
[PubMed]
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5.
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Lempicki RA, Polis MA, Yang J,
McLaughlin M, Koratich C, Huang DW, Fullmer B, Wu L, Rehm CA, Masur H,
Lane HC, Sherman KE, Fauci AS, Kottilil S. Gene Expression Profiles in
Hepatitis C Virus (HCV) and HIV Coinfection: Class Prediction Analyses
before Treatment Predict the Outcome of Anti-HCV Therapy among
HIV-Coinfected Persons. J Infect Dis. 2006 Apr 15;193(8):1172-7.
[PubMed]
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6.
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Cicala C, Arthos J, Martinelli
E, Censoplano N, Cruz CC, Chung E, Selig SM, Van Ryk D, Yang J,
Jagannatha S, Chun TW, Ren P, Lempicki RA, Fauci AS. R5 and X4 HIV
envelopes induce distinct gene expression profiles in primary
peripheral blood mononuclear cells. Proc Natl Acad Sci U S A. 2006 Mar
7;103(10):3746-51.
[PubMed]
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7.
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Di Mascio M, Sereti I, Matthews
LT, Natarajan V, Adelsberger J, Lempicki R, Yoder C, Jones E, Chow C,
Metcalf JA, Sidorov IA, Dimitrov DS, Polis MA, Kovacs JA. Naive T-cell
dynamics in human immunodeficiency virus type 1 infection: effects of
highly active antiretroviral therapy provide insights into the
mechanisms of naive T-cell depletion. J Virol. 2006
Mar;80(6):2665-74.
[PubMed]
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8.
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Patton GW, Stephens R, Sidorov
IA, Xiao X, Lempicki RA, Dimitrov DS, Shoemaker RH, Tudor G.
Transcriptomic response to differentiation induction. BMC
Bioinformatics. 2006 Feb 17;7:81.
[PubMed]
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9.
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Cicala C, Arthos J, Censoplano
N, Cruz C, Chung E, Martinelli E, Lempicki RA, Natarajan V, VanRyk D,
Daucher M, Fauci AS. HIV-1 gp120 induces NFAT nuclear translocation in
resting CD4+ T-cells. Virology. 2006 Feb 5;345(1):105-14.
[PubMed]
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10.
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Kottilil S, Shin K,
Jackson JO, Reitano KN, O'Shea MA, Yang J, Hallahan CW, Lempicki R,
Arthos J, Fauci AS. Innate immune dysfunction in HIV infection: effect
of HIV envelope-NK cell interactions. J Immunol. 2006 Jan 15;176(2):
1107-14.
[PubMed]
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2005
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1.
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Xiao X, Sidorov IA, Gee J,
Lempicki RA, Dimitrov DS. Retinoic acid-induced downmodulation of
telomerase activity in human cancer cells. Exp Mol Pathol. 2005
Oct;79(2):108-17.
[PubMed]
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2.
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Kovacs JA, Lempicki RA, Sidorov
IA, Adelsberger JW, Sereti I, Sachau W, Kelly G, Metcalf JA, Davey RT
Jr, Falloon J, Polis MA, Tavel J, Stevens R, Lambert L, Hosack DA,
Bosche M, Issaq HJ, Fox SD, Leitman S, Baseler MW, Masur H, Di Mascio
M, Dimitrov DS, Lane HC. Induction of prolonged survival of CD4+
T lymphocytes by intermittent IL-2 therapy in HIV-infected patients. J
Clin Invest. 2005 Aug;115(8):2139-48
[PubMed]
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2004
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1.
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Sereti I, Anthony KB,
Martinez-Wilson H, Lempicki R, Adelsberger J, Metcalf JA, Hallahan CW,
Follmann D, Davey RT, Kovacs JA, Lane HC. IL-2-induced CD4+ T-cell
expansion in HIV-infected patients is associated with long-term
decreases in T-cell proliferation. Blood. 2004 Aug 1;104(3):775-80.
Epub 2004 Apr 13.
[PubMed]
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2003
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1.
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Becker KG, Hosack DA, Dennis G
Jr, Lempicki RA, Bright TJ, Cheadle C, Engel J. PubMatrix: a tool
for multiplex literature mining. BMC Bioinformatics. 2003 Dec
10;4:61.
[PubMed]
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2.
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Hawse JR, Hejtmancik JF, Huang
Q, Sheets NL, Hosack DA, Lempicki RA, Horwitz J, Kantorow M.
Identification and functional clustering of global gene expression
differences between human age-related cataract and clear lenses. Mol
Vis. 2003 Oct 7;9:515-37.
[PubMed]
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3.
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Tan PK, Downey TJ, Spitznagel EL
Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC. Evaluation
of gene expression measurements from commercial microarray platforms.
Nucleic Acids Res. 2003 Oct 1;31(19):5676-84. [PubMed]
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4.
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Chun TW, Justement JS, Lempicki
RA, Yang J, Dennis G Jr, Hallahan CW, Sanford C, Pandya P, Liu S,
McLaughlin M, Ehler LA, Moir S, Fauci AS. Gene expression and
viral prodution in latently infected, resting CD4+ T cells in viremic
versus aviremic HIV-infected individuals. Proc Natl Acad Sci U S A.
2003 Feb 18;100(4):1908-13. Epub 2003 Jan 27.
[PubMed]
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5.
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Hosack DA, Dennis G Jr, Sherman
BT, Lane HC, Lempicki RA. Identifying biological themes within lists of
genes with EASE. Genome Biol. 2003;4(10):R70. Epub 2003 Sep 11.
[PubMed]
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6.
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Dennis G Jr, Sherman BT, Hosack
DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for
Annotation, Visualization, and Integrated Discovery. Genome Biol.
2003;4(5):P3. Epub 2003 Apr 3.
[PubMed]
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7.
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Hengel RL, Thaker V, Pavlick MV,
Metcalf JA, Dennis G Jr, Yang J, Lempicki RA, Sereti I, Lane HC.
Cutting edge: L-selectin (CD62L) expression distinguishes small resting
memory CD4+ T cells that preferentially respond to recall antigen. J
Immunol. 2003 Jan 1;170(1):28-32.
[PubMed]
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8.
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Imamichi T, Murphy MA,
Adelsberger JW, Yang J, Watkins CM, Berg SC, Baseler MW, Lempicki RA,
Guo J, Levin JG, Lane HC. Actinomycin D induces high-level resistance
to thymidine analogs in replication of human immunodeficiency virus
type 1 by interfering with host cell thymidine kinase expression. J
Virol. 2003 Jan;77(2):1011-20.
[PubMed]
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2002
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1.
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Xiao X, Phogat SK, Sidorov IA,
Yang J,
Horikawa I, Prieto D, Adelesberger J, Lempicki R, Barrett JC, Dimitrov
DS. Identification and characterization of rapidly dividing U937 clones
with differential telomerase activity and gene expression profiles:
role of c-Myc/Mad1 and Id/Ets proteins. Leukemia. 2002
Sep;16(9):1877-80.
[PubMed]
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2.
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Natarajan V, Lempicki RA,
Sereti I,
Badralmaa Y, Adelsberger
JW, Metcalf JA, Prieto DA, Stevens R, Baseler MW, Kovacs JA, Lane HC.
Increased
peripheral expansion of naive CD4+ T cells in vivo after IL-2 treatment
of
patients with HIV infection. Proc Natl Acad Sci U S A. 2002 Aug
6;99(16):10712-7.
[PubMed]
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3.
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Ishibe N, Prieto D, Hosack DA,
Lempicki RA,
Goldin LR, Raffeld M, Marti GE, Caporaso NE. Telomere length and
heavy-chain mutation status in familial chronic lymphocytic leukemia.
Leuk Res. 2002 Sep;26(9):791-4.
[PubMed]
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4.
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Cicala C, Arthos J, Selig SM,
Dennis G Jr,
Hosack DA, Van Ryk D, Spangler ML, Steenbeke TD, Khazanie P, Gupta N,
Yang J, Daucher M, Lempicki RA, Fauci AS. HIV envelope induces a
cascade of cell signals in non-proliferating target cells that favor
virus replication. Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9380-5.
[PubMed]
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5.
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Sidorov, I.A., Hosack, D.A.,
Gee, D., Yang,
J., Cam, M.C.,
Lempicki, R.A., Dimitrov, D.S. Oligonucleotide microarray data
distribution and
normalization, Information Sciences 2002 146(1-4): 67-73.
[Link]
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2001
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1.
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Kovacs JA, Lempicki RA, Sidorov
IA,
Adelsberger JW, Herpin B, Metcalf JA, Sereti I, Polis MA, Davey RT,
Tavel J, Falloon J, Stevens R, Lambert L, Dewar R, Schwartzentruber DJ,
Anver MR, Baseler MW, Masur H, Dimitrov DS, Lane HC. Identification of
dynamically distinct subpopulations of T lymphocytes that are
differentially affected by HIV. J Exp Med. 2001 Dec 17;194(12):1731-41.
[PubMed]
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2.
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Douek DC, Betts MR, Hill BJ,
Little SJ,
Lempicki R, Metcalf
JA, Casazza J, Yoder C, Adelsberger JW, Stevens RA, Baseler MW, Keiser
P,
Richman DD, Davey RT, Koup RA. Evidence for increased T cell turnover
and
decreased thymic output in HIV infection. J Immunol. 2001 Dec
1;167(11):6663-8.
[PubMed]
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3.
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Kovacs JA, Vogel S, Metcalf JA,
Baseler M,
Stevens R, Adelsberger J, Lempicki R, Hengel RL, Sereti I, Lambert L,
Dewar RL, Davey RT Jr, Walker RE, Falloon J, Polis MA, Masur H, Lane
HC. Interleukin-2 induced immune effects in human immunodeficiency
virus-infected patients receiving intermittent interleukin-2
immunotherapy. Eur J Immunol. 2001 May;31(5):1351-60.
[PubMed]
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4.
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(Book Chapter) D.S. Dimitrov,
I.A. Sidorov, Y.
Endo, T. Igarashi, R.A.
Lempicki, J. Kovacs, R.T. Davey, J. Lifson, M.A. Martin and H.C. Lane.
DYNAMICS
MODELS OF VIRUS/CELL TURNOVER IN HIV INFECTIONS. Proc.
Atl. Symp. Comput. Biol. Genome Information Systems and
Technology (CBGIST 2001), Eds. Wu, C.H., Wang, P.P, Wang, J.T.L.,
Durham, pp. 200-204,
2001.
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2000
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1.
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Lempicki RA, Kovacs JA, Baseler
MW,
Adelsberger JW, Dewar
RL, Natarajan V, Bosche MC, Metcalf JA, Stevens RA, Lambert LA, Alvord
WG,
Polis MA, Davey RT, Dimitrov DS, Lane HC. Impact
of HIV-1 infection and highly active antiretroviral
therapy on
the kinetics of CD4+ and CD8+ T cell turnover in HIV-infected patients.
Proc
Natl Acad Sci U S A. 2000 Dec 5;97(25):13778-83.
[PubMed]
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2.
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Carpenter S, Vaughn EM, Yang J,
Baccam P,
Roth JA, Wannemuehler
Y., Antigenic and genetic stability of bovine immunodeficiency virus
during
long-term persistence in cattle experimentally infected with the
BIV(R29)
isolate. J Gen Virol 2000 Jun;81:1463-1472.
[PubMed]
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| 1999 |
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1.
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Davey RT, Jr,Bhat N, Yoder C,
Chun TW,
Metcalf JA, Dewar R, Natarajan V, Lempicki RA, Adelsberger JW, Miller
KD, Kovacs JA, Polis MA, Walker RE, Falloon J, Masur H, Gee D, Baseler
M, Dimitrov DS, Fauci AS, Lane HC. HIV-1 and T cell dynamics after
interruption of highly active antiretroviral therapy (HAART) in
patients with a history of sustained viral suppression.
Proc Natl Acad Sci 1999 96(26):15109-14.
[PubMed]
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